Sohail Hajra, Naveed Muhammad, Aziz Tariq, El Hadi Mohamed Rania Ali, Al-Joufi Fakhria A
Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54000, Pakistan.
Laboratory of Animal Health, Hygiene and Food Quality, University of Ioannina, Arta, Greece.
Funct Integr Genomics. 2025 Aug 13;25(1):167. doi: 10.1007/s10142-025-01684-0.
This study presents the whole-genome sequencing and comprehensive analysis of Bacillus subtilis MBBL2, a strain isolated from soil samples in Lahore, Pakistan. The genome consists of 4,574,405 base pairs, with a GC content of 42.99%, and is assembled into 908 contigs. Using a range of bioinformatics tools, we performed genome assembly, functional annotation, secondary metabolite biosynthesis prediction, antimicrobial resistance (AMR) gene identification, and CRISPR array detection. The genome was initially assembled, achieving an average coverage of 126.534x, and its quality was also assessed to ensure completeness. Prokka was used to annotate 5,392 genes, including 5,033 protein-coding sequences, tRNAs, and rRNAs. Secondary metabolite biosynthesis clusters were identified revealing several important clusters involved in riboflavin, vitamin B6 biosynthesis, and antimicrobial peptide production via non-ribosomal peptide synthetase (NRPS). Notably, a novel bacteriocin gene cluster was detected, suggesting the strain's potential as a source of antimicrobial peptides. AMR genes were identified highlighting resistance to various antibiotics. CRISPR arrays were also analyzed indicating the strain's adaptive immune system. Genomic comparisons provided insights into the genetic diversity and evolutionary relationships of Bacillus subtilis strains. This study reveals the potential of B. subtilis MBBL2 as a probiotic in aquaculture, with applications in sustainable practices such as biocontrol. The findings contribute valuable genomic resources to the B. subtilis research community and open avenues for future biotechnological applications.
本研究展示了枯草芽孢杆菌MBBL2的全基因组测序及综合分析，该菌株从巴基斯坦拉合尔的土壤样本中分离得到。基因组由4,574,405个碱基对组成，GC含量为42.99%，组装成908个重叠群。我们使用一系列生物信息学工具进行了基因组组装、功能注释、次生代谢物生物合成预测、抗菌抗性（AMR）基因鉴定和CRISPR阵列检测。首先对基因组进行组装，平均覆盖度达到126.534倍，同时评估其质量以确保完整性。使用Prokka对5,392个基因进行注释，包括5,033个蛋白质编码序列、tRNA和rRNA。鉴定出次生代谢物生物合成簇，揭示了几个参与核黄素、维生素B6生物合成以及通过非核糖体肽合成酶（NRPS）产生抗菌肽的重要簇。值得注意的是，检测到一个新的细菌素基因簇，表明该菌株作为抗菌肽来源的潜力。鉴定出AMR基因，突出了对各种抗生素的抗性。还分析了CRISPR阵列，表明该菌株的适应性免疫系统。基因组比较为枯草芽孢杆菌菌株的遗传多样性和进化关系提供了见解。本研究揭示了枯草芽孢杆菌MBBL2作为水产养殖益生菌的潜力，可应用于生物防治等可持续实践。这些发现为枯草芽孢杆菌研究界提供了宝贵的基因组资源，并为未来的生物技术应用开辟了道路。
